0000000000124125
AUTHOR
Alfredo Sánchez De Merás
showing 42 related works from this author
Electronic structure of the ground and excited states of beta-carboline.
2008
Coupled-cluster calculations are used to compute the energy of conversion between the neutral and the zwitterionic forms of beta-carboline. The stability of the different species is discussed in terms of charge separation and aromatic character, which is related to magnetic criteria. By means of a linear response formalism the vertical excitation energies and oscillator strengths of the lowest singlet states of both structures as well as of the cationic species are determined. General agreement of the relative position and intensity of the different peaks with experimental data is achieved, but the overall spectra are slightly displaced because of solvent effects.
Understanding the ring current effects on magnetic shielding of hydrogen and carbon nuclei in naphthalene and anthracene
2008
The local response to an external magnetic field normal to the molecular plane of naphthalene and anthracene was investigated via current density and magnetic shielding density maps. The Biot-Savart law shows that the deshielding caused by pi-ring currents in naphthalene is stronger for alpha- than for beta-protons due to geometrical factors. The shielding tensor of the carbon nuclei in both molecules is strongly anisotropic and its out-of-plane component determines the up-field chemical shift of (13)C in nuclear magnetic resonance spectra. The pi-ring currents flowing beyond the C-skeleton in front of a probe carbon nucleus, and on remote parts of the molecular perimeter, yield positive co…
Polarizability and optical rotation calculated from the approximate coupled cluster singles and doubles CC2 linear response theory using cholesky dec…
2004
A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model using Cholesky decomposition of the two-electron integrals is presented. Significantly reducing storage demands and computational effort without sacrificing accuracy compared to the conventional model, the algorithm is well suited for large-scale applications. Extensive basis set convergence studies are presented for the static and frequency-dependent electric dipole polarizability of benzene and C60, and for the optical rotation of CNOFH2 and (−)-trans-cyclooctene (TCO). The origin-dependence of the optical rotation is calculated and shown to persist for CC2 even at basis set convergence. …
The CCSD(T) model with Cholesky decomposition of orbital energy denominators
2010
A new implementation of the coupled cluster singles and doubles with approximate triples correction method [CCSD(T)] using Cholesky decomposition of the orbital energy denominators is described. The new algorithm reduces the scaling of CCSD(T) from N-7 to N-6, where N is the number of orbitals. The Cholesky decomposition is carried out using simple analytical expressions that allow us to evaluate a priori the order in which the decomposition should be carried out and to obtain the relevant parts of the vectors whenever needed in the calculation. Several benchmarks have been carried out comparing the performance of the conventional and Cholesky CCSD(T) implementations. The Cholesky implement…
Grand Canonical Monte Carlo Simulations to Determine the Optimal Interlayer Distance of a Graphene Slit-Shaped Pore for Adsorption of Methane, Hydrog…
2021
The adsorption—for separation, storage and transportation—of methane, hydrogen and their mixture is important for a sustainable energy consumption in present-day society. Graphene derivatives have proven to be very promising for such an application, yet for a good design a better understanding of the optimal pore size is needed. In this work, grand canonical Monte Carlo simulations, employing Improved Lennard–Jones potentials, are performed to determine the ideal interlayer distance for a slit-shaped graphene pore in a large pressure range. A detailed study of the adsorption behavior of methane, hydrogen and their equimolar mixture in different sizes of graphene pores is obtained through ca…
MCSCF determination of the KO molecule ground state.
1992
Abstract Ab initio calculations at the MC/CASSCF level are used to determine in an accurate way the nature and position of the ground state of the KO molecule. The characteristic 2 Π and 2 Σ + alkali monoxide ionic states show a theoretical energy separation of about 0.04 eV, which produces opposite results by authors in favour of one or the other symmetry. We test the basis set dependence and active space dependence of the calculated energetical ordering of both states, with an extensive study of the active orbitais selection; the results show a ground state of 2 Σ + symmetry.
Size-intensive decomposition of orbital energy denominators
2000
We introduce an alternative to Almlöf and Häser’s Laplace transform decomposition of orbital energy denominators used in obtaining reduced scaling algorithms in perturbation theory based methods. The new decomposition is based on the Cholesky decomposition of positive semidefinite matrices. We show that orbital denominators have a particular short and size-intensive Cholesky decomposition. The main advantage in using the Cholesky decomposition, besides the shorter expansion, is the systematic improvement of the results without the penalties encountered in the Laplace transform decomposition when changing the number of integration points in order to control the convergence. Applications will…
Origin invariant calculation of optical rotation without recourse to London orbitals
2004
We propose an inherently origin invariant formulation of specific optical rotation obtained from the conventional velocity gauge expression by subtracting the static limit from the electric dipole-magnetic dipole polarizability: ããpâ,LâããÏâããpâ,LâããÏ-ããpâ,Lâãã0. London (gauge including) atomic orbitals are therefore not needed to ensure origin invariance and, consequently, this modified velocity gauge formulation may be employed in conjunction with variational and non-variational quantum chemical methods alike. Sample calculations on S-propylene oxide and 3,4- methylenedioxymethamphetamine using self-consistent field and coupled cluster wave functions…
Method specific Cholesky decomposition : Coulomb and exchange energies
2008
We present a novel approach to the calculation of the Coulomb and exchange contributions to the total electronic energy in self consistent field and density functional theory. The numerical procedure is based on the Cholesky decomposition and involves decomposition of specific Hadamard product matrices that enter the energy expression. In this way, we determine an auxiliary basis and obtain a dramatic reduction in size as compared to the resolution of identity (RI) method. Although the auxiliary basis is determined from the energy expression, we have complete control of the errors in the gradient or Fock matrix. Another important advantage of this method specific Cholesky decomposition is t…
Dissociation energies within selected configuration interaction and perturbation theory
1993
Abstract Selected configuration interaction (CI) calculations and second-order perturbational theory are used to truncate systematically multireference single and double excitation CI (MRCI) expansions in the calculation of the bond dissociation energies of several systems like the single-bonded LiF molecule or the multiple-bonded N2, NO and O2 diatomic systems. The method is extended to compute the CH bond dissociation energy ofethene C2H4. It is shown how the proposed scheme (perturbation-selected MRCI (MRCI-PS)) is able to reproduce the accuracy of complete MRCI expansions with only a small number of configurations variationally evaluated.
A computational study of some electric and magnetic properties of gaseous BF3 and BCl3
2005
We present the results of an extended computational study of the electric and magnetic properties connected to Cotton-Mouton birefringences, on the trifluoro- and trichloroborides in the gas phase. The electric dipole polarizabilities, magnetizabilities, quadrupole moments, and higher-order hypersusceptibilities—expressed as quadratic and cubic frequency-dependent response functions—are computed within Hartree-Fock, density-functional, and coupled-cluster response theories employing singly and doubly augmented correlation-consistent basis sets and London orbitals in the magnetic property calculations. The results, which illustrate the capability of time-dependent density-functional theory f…
The Dalton quantum chemistry program system
2013
Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, confi ...
Calculation of size‐intensive transition moments from the coupled cluster singles and doubles linear response function
1994
Coupled cluster singles and doubles linear response (CCLR) calculations have been carried out for excitation energies and dipole transition strengths for the lowest excitations in LiH, CH+, and C4and the results compared with the results from a CI-like approach to equation of motion coupled cluster (EOMCC). The transition strengths are similar in the two approaches for single molecule calculations on small systems. However, the CCLR approach gives size-intensive dipole transition strengths, while title EOMCC formalism does not. Thus, EOMCC calculations can give unphysically dipole transition strengths, e.g., in EOMCC calculations on a sequence of noninteracting LiH systems we obtained a neg…
Cholesky decomposition-based definition of atomic subsystems in electronic structure calculations
2010
Decomposing the Hartree-Fock one-electron density matrix and a virtual pseudodensity matrix, we obtain an orthogonal set of normalized molecular orbitals with local character to be used in post-Hartree-Fock calculations. The applicability of the procedure is illustrated by calculating CCSD(T) energies and CCSD molecular properties in reduced active spaces. © 2010 American Institute of Physics.
A coupled cluster calculation of the spectrum of urea
2001
Several coupled cluster methods have been used to compute the vertical excitation energies and oscillator strengths of the lowest singlet states of urea. Except for one excitation, the results are in good agreement with experiment, but previously non-detected transitions have been found.
Fast noniterative orbital localization for large molecules
2006
We use Cholesky decomposition of the density matrix in atomic orbital basis to define a new set of occupied molecular orbital coefficients. Analysis of the resulting orbitals ("Cholesky molecular orbitals") demonstrates their localized character inherited from the sparsity of the density matrix. Comparison with the results of traditional iterative localization schemes shows minor differences with respect to a number of suitable measures of locality, particularly the scaling with system size of orbital pair domains used in local correlation methods. The Cholesky procedure for generating orthonormal localized orbitals is noniterative and may be made linear scaling. Although our present implem…
Cholesky decomposition techniques in electronic structure theory
2011
We review recently developed methods to efficiently utilize the Cholesky decomposition technique in electronic structure calculations. The review starts with a brief introduction to the basics of the Cholesky decomposition technique. Subsequently, examples of applications of the technique to ab inito procedures are presented. The technique is demonstrated to be a special type of a resolution-of-identity or density-fitting scheme. This is followed by explicit examples of the Cholesky techniques used in orbital localization, computation of the exchange contribution to the Fock matrix, in MP2, gradient calculations, and so-called method specific Cholesky decomposition. Subsequently, examples o…
π-Ring currents in doped coronenes with nitrogen and boron: diatropic-paratropic duality.
2015
The change in the electronic structure of coronene upon doping with nitrogen or boron has been theoretically studied by means of its magnetic properties and magnetic field induced current density maps. The addition of two atoms of nitrogen or boron to the central ring of coronene causes a drastic variation in the delocalization of π-electrons, which does not depend on its nature but instead on its position. Then, doping in the para position makes coronene more aromatic while doping in the meta position makes it to become antiaromatic. The magnetic behavior of the pristine molecule is characterized by two concentric currents flowing in opposite senses that are converted into hemi-perimetric …
Large-scale calculations of excitation energies in coupled cluster theory: The singlet excited states of benzene
1996
Algorithms for calculating singlet excitation energies in the coupled cluster singles and doubles (CCSD) model are discussed and an implementation of an atomic-integral direct algorithm is presented. Each excitation energy is calculated at a cost comparable to that of the CCSD ground-state energy. Singlet excitation energies are calculated for benzene using up to 432 basis functions. Basis-set effects of the order of 0.2 eV are observed when the basis is increased from augmented polarized valence double-zeta (aug-cc-pVDZ) to augmented polarized valence triple-zeta (aug-cc-pVTZ) quality. The correlation problem is examined by performing calculations in the hierarchy of coupled cluster models…
Variation of polarizability in the [4n+2] annulene series: from [22]- to [66]-annulene.
2008
Using correlated ab initio methods, the polarizability of large [4n + 2]-annulenes is determined, showing that there exists an almost linear relation between the exaltation of magnetic susceptibility (a measure of aromaticity) and an equivalent enlargement of polarizability.
A mutliconfigurational study of low-lying electronic states of KO
1992
Abstract Potential energy curves and spectroscopic parameters of several electronic states of the KO molecule have been calculated using multi-configurational methods. The KO B 2Π state, first time theoretically described, presents a strong avoided crossing with the A 2Π state, and allows for the explanation of the observed fluorescence of the KO molecule. Eleven electronic states have been studied at all the internuclear distances. Effects of complete active space and basis set selections on the results are also analyzed.
Energy interactions in amyloid-like fibrils from NNQQNY.
2014
We use large-scale MP2 calculations to analyze the interactions appearing in amyloid fibers, which are difficult to determine experimentally. To this end, dimers and trimers of the hexapeptide NNQQNY from the yeast prion-like protein Sup35 were considered as model systems. We studied the energy interactions present in the three levels of organization in which the formation of amyloid fibrils is structured. The structural changes in the hydrogen bonds were studied too. It was found that the most energetic process is the formation of the β-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of t…
Modeling the Interaction of Carbon Monoxide with Flexible Graphene: From Coupled Cluster Calculations to Molecular-Dynamics Simulations
2018
The interaction of CO with graphene was studied at different theoretical levels. Quantum-mechanical calculations on finite graphene models with the use of coronene for coupled cluster calculations and circumcoronene for B97D calculations showed that there was no preferential site for adsorption and that the most important factor was the orientation of CO relative to graphene. The parallel orientation was preferred, with binding energies around 9 kJ mol-1 at the CCSD(T) and B97D levels, which was in good agreement with experimental findings. From a large number of CO-circumcoronene and CO-CO interactions, computed at different distances and randomly generated orientations, parameters were fi…
Lower Rydberg series of methane: a combined coupled cluster linear response and molecular quantum defect orbital calculation.
2006
Vertical excitation energies as well as related absolute photoabsorption oscillator strength data are very scarce in the literature for methane. In this study, we have characterized the three existing series of low-lying Rydberg states of CH4 by computing coupled cluster linear response (CCLR) vertical excitation energies together with oscillator strengths in the molecular-adapted quantum defect orbital formalism from a distorted Cs geometry selected on the basis of outer valence green function calculations. The present work provides a wide range of data of excitation energies and absolute oscillator strengths which correspond to the Rydberg series converging to the three lower ionization p…
Reduced scaling in electronic structure calculations using Cholesky decompositions
2003
The small numerical rank of the two-electron integral matrix for large molecular systems and large basis sets was demonstrated. Though, the current implementation still requires some improvements on the calculations done in the inner most loop of the decomposition do not exploit the parsity in the Cholesky vectors. With respect to the practical applicability of the presented method an efficient approach to geometrical derivatives was imperative. Such an approach was obtained including certain derivative product functions and decomposing an expanded integral matrix.
Nitrogen Gas on Graphene: Pairwise Interaction Potentials
2018
We investigate different types of potential parameters for the graphene-nitrogen interaction. Interaction energies calculated at DFT level are fitted with the semi-emperical Improved Lennard-Jones potential. Both a pseudo-atom potential and a full atomistic potential are considered. Furthermore, we consider the influence of the electrostatic part on the parameters using different charge schemes found in the literature as well as optimizing the charges ourselves. We have obtained parameters for both the nitrogen dimer and the graphene-nitrogen system. For the former, the four-charges Cracknell scheme reproduces with high precision the CCSD(T) interaction energy as well as the experimental di…
Calculation of excitation energies from the CC2 linear response theory using Cholesky decomposition
2014
A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model is reported. It employs a Cholesky decomposition of the two-electron integrals that significantly reduces the computational cost and the storage requirements of the method compared to standard implementations. Our algorithm also exploits a partitioning form of the CC2 equations which reduces the dimension of the problem and avoids the storage of doubles amplitudes. We present calculation of excitation energies of benzene using a hierarchy of basis sets and compare the results with conventional CC2 calculations. The reduction of the scaling is evaluated as well as the effect of the Cholesky …
Magnetic field-induced alignment of molecular rotor-shaped cyclophanes
2010
Molecular pinwheels consisting of dipolar substituted cyclophanes in solution can function as free microscopic rotors in the presence of a homogeneous static magnetic field B and a circularly polarized electric field E rotating on a plane containing B. Owing to the high magnetic anisotropy of [26](1,2,3,4,5,6)cyclophane and [36](1,2,3,4,5,6)cyclophane biased by strong ring currents, ∼1 in 105 molecules are expected to align with the C6 symmetry axis perpendicular to a magnetic field of 21 T. The magnetic-field-controlled alignment of rotor-shaped cyclophanes is insignificantly affected by nonpolar solvents, for example, toluene.
Accurate ab initio density fitting for multiconfigurational self-consistent field methods
2008
Using Cholesky decomposition and density fitting to approximate the electron repulsion integrals, an implementation of the complete active space self-consistent field (CASSCF) method suitable for large-scale applications is presented. Sample calculations on benzene, diaquo-tetra- μ -acetato-dicopper(II), and diuraniumendofullerene demonstrate that the Cholesky and density fitting approximations allow larger basis sets and larger systems to be treated at the CASSCF level of theory with controllable accuracy. While strict error control is an inherent property of the Cholesky approximation, errors arising from the density fitting approach are managed by using a recently proposed class of auxi…
Multi-level coupled cluster theory
2014
We present a general formalism where different levels of coupled cluster theory can be applied to different parts of the molecular system. The system is partitioned into subsystems by Cholesky decomposition of the one-electron Hartree-Fock density matrix. In this way the system can be divided across chemical bonds without discontinuities arising. The coupled cluster wave function is defined in terms of cluster operators for each part and these are determined from a set of coupled equations. The total wave function fulfills the Pauli-principle across all borders and levels of electron correlation. We develop the associated response theory for this multi-level coupled cluster theory and prese…
A coupled-cluster study of lanthanum trihalide structures
2002
Coupled-cluster calculations were carried at the CCSD(T)-level in order to determine the structures and vibrational spectra of the lanthanum trihalides LaF3 and LaCl3. Two different approaches were employed to describe scalar relativistic effects; the quasi-relativistic Effective Core Potential approach and the all-electron Douglas–Kroll approach. We find LaF3 to be of pyramidal structure and LaCl3 to be planar. The obtained vibrational frequencies accord well with experimental measurements except for the ν2 mode. This disagreement is attributed to the intrinsic uncertainty of harmonic frequencies of this fluxional mode as extracted from spectra which were obtained at high temperature and f…
Restricted and complete-active-space multiconfiguration linear response calculations of the polarizability of formamide and urea
1991
Abstract Using the polarized basis sets of Sadlej, we have carried out multiconfiguration linear response (MCLR) calculations of static and dynamic polarizabilities of water, carbon dioxide, formamide and urea. It is found that the polarized basis sets give a good description of the polarizabilities. The uncorrelates (self-consistent field) polarizabilities are in general 10% or more lower than the experimental values. The correlation as introduced in the complete-active-space (CAS) and restricted-active-space (RAS) MCLR calculations recovers the major part of this deviation.
Theoretical Study on the Structures and Electronic Spectra of TCNE2−
2006
Investigations into the charge-separated states and electron-transfer transitions in tetracyanoethylene (TCNE) compiles have recently generated much interest. In this work we present theoretical calculations showing that the most stable structure of the dianion TCNE 2- has D 2d symmetry in vacuum as well as in the solvents dichloromethane and cicetonitrile. By means of the coupled cluster linear response, we compute the vertical electronic spectrum in both the gas phase and solution. The theoreitcal results, are compared to the experimental data and good agreement is achieved.
Structure, magnetizability, and nuclear magnetic shielding tensors of bis-heteropentalenes. IV. Dihydrophospholophosphole isomers
2005
The geometry of the heteropentalenes formed by two phosphole units has been determined at the DFT level. The magnetic susceptibility and the nuclear magnetic shielding at the nuclei of these systems have also been calculated using gauge-including atomic orbitals and a large Gaussian basis set to achieve near Hartree-Fock estimates. A comparative study of the various isomers, of their flattened analogs, and of the parent phosphole molecule, shows that the [3,4-c] isomer is the most aromatic system in the set considered, assuming diatropicity and degree of planarity as indicators, even if it is the less stable in terms of total molecular energy. Plots of magnetic field-induced current densiti…
Flexibility in the Graphene Sheet: The Influence on Gas Adsorption from Molecular Dynamics Studies
2019
Despite being considered completely rigid in most studies, graphene is really flexible leading to out-of-plane movements. In this work, the influence of such flexibility on the adsorption of methane and nitrogen on graphene is studied using molecular dynamics. Indeed, we have used intramolecular force fields for graphene with in-plane and out-of-plane components that allow for describing the movements and deformations of the graphene sheets and providing a more realistic description of the adsorbent. In addition, intermolecular force fields validated at the CCSD(T) level are used. We show that considering the movement of graphene in the adsorption study significantly improves the performanc…
The vertical spectrum of H2CO revisited: (SC)2-CI and CC calculations
2003
The vertical electronic spectrum of formaldehyde has been studied by means of (SC)2-MR-SDCI and CCLR methods. Two basis sets of atomic natural orbitals (ANOs) complemented with a one-centre series of Rydberg orbitals were used. The first was taken from the CASPT2 study by Merchan, M., and Roos, B. O., 1995, Theoret. Chim. Acta, 92, 221, and may be described as C,O[4s3pld]/H[2slp] with a lslpld Rydberg series centred in the charge centroid of the 2B2 state of the cation. The second was a larger basis set that may be described as C,O[6s5p3d2f]/H[4s3p2d] + 3s3p3d in the same centre. The (SC)2 dressing may be applied efficiently to an MR-SDCI method and comparison with the dressed CAS-SDCI is s…
The integral‐direct coupled cluster singles and doubles model
1996
An efficient and highly vectorized implementation of the coupled cluster singles and doubles (CCSD) model using a direct atomic integral technique is presented. The minimal number of n6processes has been implemented for the most time consuming terms and point group symmetry is used to further reduce operation counts and memory requirements. The significantly increased application range of the CCSD method is illustrated with sample calculations on several systems with more than 500 basis functions. Furthermore, we present the basic trends of an open ended algorithm and discuss the use of integral prescreening. © 1996 American Institute of Physics.
From Pentalene to Dicyclopenta[b,g]naphthalene, or the Change towards Delocalized Structures
2005
Lining triples-corrected coupled-cluster methods as well as other high-level theoretical approximations, the optimized parameters and isomerization barriers of the family of compounds cyclopentadiene-(benzene) x -cyclopentadiene (x 0, 1, 2) are computed. In contrast to previous studies, s-indacene presents a localized C 2 h geometry. Also, the localized structure of pentalene is found to be the most stable, but when two benzene rings are intercalated between the five-member rings of pentalene, the resulting molecule preferably adopts a delocalized D 2 h conformation.
Molecular dynamics of CH4/N2 mixtures on a flexible graphene layer: adsorption and selectivity case study
2019
We theoretically investigate graphene layers, proposing them as membranes of subnanometer size suitable for CH4/N2 separation and gas uptake. The observed potential energy surfaces, representing the intermolecular interactions within the CH4/N2 gaseous mixtures and between these and the graphene layers, have been formulated by adopting the so-called Improved Lennard-Jones (ILJ) potential, which is far more accurate than the traditional Lennard-Jones potential. Previously derived ILJ force fields are used to perform extensive molecular dynamics simulations on graphene's ability to separate and adsorb the CH4/N2 mixture. Furthermore, the intramolecular interactions within graphene were explic…
Coupled cluster calculations of the vertical excitation energies of tetracyanoethylene
2003
The vertical spectrum of tetracyanoethylene was studied using coupled cluster theory. It was found that the lowest singlet-singlet transition, which corresponds to the excitation from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO) excitation, occurs at 5.16 eV in the gas phase and is lowered approximately 0.1 eV due to solvent effects in acetonitrile. A parallel study on the ethene spectrum showed the quality of the basis sets and methods used, by placing the V state 7.92 eV above the ground state and giving an energy for the 0-0 transition of 5.42 eV to be compared with the experimental value of 5.50 eV.
Coupled cluster calculations of interaction energies in benzene–fluorobenzene van der Waals complexes
2007
Benzene-fluorobenzene complexes are used as model systems to simulate the interactions of the SBB-HCAII protein-ligand complex. Using the second-order Moller-Plesset [MP2] and the coupled cluster singles and doubles including connected triple excitations models recently implemented with Cholesky decompositions we evaluate accurate interaction energies for several benzene-fluorobenzene van der Waals complexes. We consider edge-to-face interactions and compare the results to those from a recent MP2 study and to experimental findings. In contrast to experimental trends, we find that the interaction tends to decrease with increasing fluorination and conclude that benzene-fluorobenzene complexes…
How nitrogen modifies the nuclear magnetic shielding in tetraazanaphthalenes
2009
Although for planar conjugated hydrocarbons the out-of-plane component of proton magnetic shielding is an unquestionable quantitative aromaticity indicator, the same is not true for tetraazanaphthalenes. As in these compounds the (core + sigma)-currents associated to the nitrogen nuclei diminish the perpendicular component of shielding, abnormal values of (1)H NMR sigma(zz) are obtained. Therefore, a consistent aromaticity measure must be based only on the pi-contribution to the out-of-plane component of proton magnetic shielding. Otherwise, the behavior of these compounds in presence of an external magnetic field parallels that of naphthalene, with the nitrogen nuclei contributing to the r…